The aim of this work was to measure the concentration of the indoor radon in 16 Portuguese thermal spas (38% of the thermal spas in Portugal) and assess its variability within each establishment as well as its contribution to the effective dose. The measurements were performed with CR-39 passive detectors placed at different workplaces within each thermal spa, for an average period of 42 days, in different seasons of the year. The indoor radon concentrations ranged from 68 to 4335 Bq/m3 with a geometric mean of 437 Bq/m3 and an arithmetic mean of 702 Bq/m3. Geological factors that can lead to such behaviour are discussed. The results showed that the EU reference level of 300 Bq/m3 (Directive 2013/59/EURATOM) was exceeded in several cases. No significant differences were observed among measurements taken during different seasons of the year, however, large differences of radon concentrations in different rooms of the same thermal establishment were noted as well as signiﬁcant difference when comparing to other thermal establishments. The effective dose resulting from the inhalation of radon ranged between 2 and 32 mSv/y. In 43% of the thermal spas, the effective dose is likely to be higher than 6 mSv/y, which means that the exposure should be managed as a “planned exposure situation” according to the European Directive 2013/59/EURATOM. Also, in 19% of the cases, the annual effective dose exceeds 20 mSv/y, and in these cases, monitoring and radiological protection is required as laid down in the European Directive 2013/59/EURATOM.